src/flucq/FluctuatingChargeObjectiveFunction.cpp

/*
 * Copyright (c) 2012 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#include "flucq/FluctuatingChargeObjectiveFunction.hpp"

namespace OpenMD{
  
  FluctuatingChargeObjectiveFunction::FluctuatingChargeObjectiveFunction(SimInfo* info, ForceManager* forceMan, FluctuatingChargeConstraints* fqConstraints)
    : info_(info), forceMan_(forceMan), fqConstraints_(fqConstraints), 
      thermo(info) {       
  }
  
  RealType FluctuatingChargeObjectiveFunction::value(const DynamicVector<RealType>& x) {
    setCoor(x);
    forceMan_->calcForces();

    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    potVec pot = curSnapshot->getLongRangePotentials();
    potVec exPot = curSnapshot->getExcludedPotentials();  
  
    return pot[ELECTROSTATIC_FAMILY] + exPot[ELECTROSTATIC_FAMILY];
  }
  
  void FluctuatingChargeObjectiveFunction::gradient(DynamicVector<RealType>& grad, const DynamicVector<RealType>& x) {
    
    setCoor(x);     
    
    forceMan_->calcForces(); 
    fqConstraints_->applyConstraints();

    getGrad(grad);      
  }
  
  RealType FluctuatingChargeObjectiveFunction::valueAndGradient(DynamicVector<RealType>& grad,
                                                              const DynamicVector<RealType>& x) {

    setCoor(x);     

    forceMan_->calcForces();
    fqConstraints_->applyConstraints();
    
    getGrad(grad); 

    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    potVec pot = curSnapshot->getLongRangePotentials();
    potVec exPot = curSnapshot->getExcludedPotentials();    

    return pot[ELECTROSTATIC_FAMILY] + exPot[ELECTROSTATIC_FAMILY];
  }
  
  void FluctuatingChargeObjectiveFunction::setCoor(const DynamicVector<RealType> &x) const {
    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    int index = 0;
    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {
      
      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {
       
        atom->setFlucQPos(x[index++]);
      }
    }    
  }
  
  void FluctuatingChargeObjectiveFunction::getGrad(DynamicVector<RealType> &grad) {
    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    
    int index = 0;
    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {

      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {

        grad[index++] = -atom->getFlucQFrc();
      }
    }
  }

  DynamicVector<RealType> FluctuatingChargeObjectiveFunction::setInitialCoords() {
    SimInfo::MoleculeIterator i;
    Molecule::FluctuatingChargeIterator  j;
    Molecule* mol;
    Atom* atom;
    
    int index = 0;    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {

      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {
        
        index++;
      }
    }

    DynamicVector<RealType> initCoords(index);
    index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {

      for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
           atom = mol->nextFluctuatingCharge(j)) {
        
        initCoords[index++] = atom->getFlucQPos();
      }
    }   
    return initCoords;
  }
}
Revision:	1929
Committed:	Mon Aug 19 13:12:00 2013 UTC (11 years, 8 months ago) by gezelter
File size:	5642 byte(s)
Log Message:	Backing out fluc-rho and putting back the Electrostatic fluctuating charge with coulomb integrals for atoms within a region.
#	Content
1	/*
2	* Copyright (c) 2012 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#include "flucq/FluctuatingChargeObjectiveFunction.hpp"
44
45	namespace OpenMD{
46
47	FluctuatingChargeObjectiveFunction::FluctuatingChargeObjectiveFunction(SimInfo* info, ForceManager* forceMan, FluctuatingChargeConstraints* fqConstraints)
48	: info_(info), forceMan_(forceMan), fqConstraints_(fqConstraints),
49	thermo(info) {
50	}
51
52	RealType FluctuatingChargeObjectiveFunction::value(const DynamicVector<RealType>& x) {
53	setCoor(x);
54	forceMan_->calcForces();
55
56	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
57	potVec pot = curSnapshot->getLongRangePotentials();
58	potVec exPot = curSnapshot->getExcludedPotentials();
59
60	return pot[ELECTROSTATIC_FAMILY] + exPot[ELECTROSTATIC_FAMILY];
61	}
62
63	void FluctuatingChargeObjectiveFunction::gradient(DynamicVector<RealType>& grad, const DynamicVector<RealType>& x) {
64
65	setCoor(x);
66
67	forceMan_->calcForces();
68	fqConstraints_->applyConstraints();
69
70	getGrad(grad);
71	}
72
73	RealType FluctuatingChargeObjectiveFunction::valueAndGradient(DynamicVector<RealType>& grad,
74	const DynamicVector<RealType>& x) {
75
76	setCoor(x);
77
78	forceMan_->calcForces();
79	fqConstraints_->applyConstraints();
80
81	getGrad(grad);
82
83	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
84	potVec pot = curSnapshot->getLongRangePotentials();
85	potVec exPot = curSnapshot->getExcludedPotentials();
86
87	return pot[ELECTROSTATIC_FAMILY] + exPot[ELECTROSTATIC_FAMILY];
88	}
89
90	void FluctuatingChargeObjectiveFunction::setCoor(const DynamicVector<RealType> &x) const {
91	SimInfo::MoleculeIterator i;
92	Molecule::FluctuatingChargeIterator j;
93	Molecule* mol;
94	Atom* atom;
95	int index = 0;
96
97	for (mol = info_->beginMolecule(i); mol != NULL;
98	mol = info_->nextMolecule(i)) {
99
100	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
101	atom = mol->nextFluctuatingCharge(j)) {
102
103	atom->setFlucQPos(x[index++]);
104	}
105	}
106	}
107
108	void FluctuatingChargeObjectiveFunction::getGrad(DynamicVector<RealType> &grad) {
109	SimInfo::MoleculeIterator i;
110	Molecule::FluctuatingChargeIterator j;
111	Molecule* mol;
112	Atom* atom;
113
114	int index = 0;
115
116	for (mol = info_->beginMolecule(i); mol != NULL;
117	mol = info_->nextMolecule(i)) {
118
119	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
120	atom = mol->nextFluctuatingCharge(j)) {
121
122	grad[index++] = -atom->getFlucQFrc();
123	}
124	}
125	}
126
127	DynamicVector<RealType> FluctuatingChargeObjectiveFunction::setInitialCoords() {
128	SimInfo::MoleculeIterator i;
129	Molecule::FluctuatingChargeIterator j;
130	Molecule* mol;
131	Atom* atom;
132
133	int index = 0;
134	for (mol = info_->beginMolecule(i); mol != NULL;
135	mol = info_->nextMolecule(i)) {
136
137	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
138	atom = mol->nextFluctuatingCharge(j)) {
139
140	index++;
141	}
142	}
143
144	DynamicVector<RealType> initCoords(index);
145	index = 0;
146	for (mol = info_->beginMolecule(i); mol != NULL;
147	mol = info_->nextMolecule(i)) {
148
149	for (atom = mol->beginFluctuatingCharge(j); atom != NULL;
150	atom = mol->nextFluctuatingCharge(j)) {
151
152	initCoords[index++] = atom->getFlucQPos();
153	}
154	}
155	return initCoords;
156	}
157	}